rs1515024

Variant names:

• chrX-79559798-T-C
• rs1515024

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.109 in 111,216 control chromosomes in the GnomAD database, including 625 homozygotes. There are 3,761 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (625 hom., 3761 hem., cov: 23)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.109 AC: 12068 AN: 111162 Hom.: 623 Cov.: 23

Gnomad AFR AF: 0.0210

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.0827

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.0214

Gnomad SAS AF: 0.361

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.103

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.109 AC: 12075 AN: 111216 Hom.: 625 Cov.: 23 AF XY: 0.112 AC XY: 3761 AN XY: 33650

African (AFR) AF: 0.0209 AC: 649 AN: 31008

American (AMR) AF: 0.0826 AC: 864 AN: 10456

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 333 AN: 2629

East Asian (EAS) AF: 0.0215 AC: 77 AN: 3581

South Asian (SAS) AF: 0.363 AC: 966 AN: 2660

European-Finnish (FIN) AF: 0.218 AC: 1308 AN: 5991

Middle Eastern (MID) AF: 0.143 AC: 31 AN: 217

European-Non Finnish (NFE) AF: 0.144 AC: 7558 AN: 52488

Other (OTH) AF: 0.105 AC: 159 AN: 1509

Alfa AF: 0.133 Hom.: 8706

Bravo AF: 0.0948

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.055
DANN	Benign	0.53
PhyloP100		-1.4

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1515024; hg19: chrX-78815295;